Genetic alterations in isocitrate dehydrogenase and other genes in malignant glioma

Patent metadata

Field	Value
Publication number	US-9353418-B2
Application number	US-201314102730-A
Country	US
Kind code	B2
Filing date	Dec 11, 2013
Priority date	Sep 3, 2008
Publication date	May 31, 2016
Grant date	May 31, 2016

Abstract

We found mutations of the R132 residue of isocitrate dehydrogenase 1 (IDH1) in the majority of grade II and III astrocytomas and oligodendrogliomas as well as in glioblastomas that develop from these lower grade lesions. Those tumors without mutations in IDH1 often had mutations at the analogous R172 residue of the closely related IDH2 gene. These findings have important implications for the pathogenesis and diagnosis of malignant gliomas.

First claim

We claim:

1. A composition comprising an isolated pair of polynucleotide primers comprising at least 10 but less than 600 contiguous nucleotide residues of a coding sequence of a human IDH1 or IDH2 protein found in a human tumor or its complement, wherein at least one of said primers is labeled with a detectable label, wherein in one of said pair of polynucleotide primers said at least 10 contiguous nucleic acid residues comprise:
nucleotides 394 and/or 395 of IDH1 coding sequence, wherein said nucleotides are not C or T at nucleotide 394 and/or not G at nucleotide 395, respectively;
nucleotide 515 of IDH2 coding sequence, wherein said nucleotide 515 is not a G;
the complement of nucleotides 394 and/or 395 of IDH1 coding sequence, wherein said nucleotides are not G or A at the complement of nucleotide 394 and/or not C at the complement of nucleotide 395, respectively; or
the complement of nucleotide 515 of IDH2 coding sequence, wherein said complement of nucleotide 515 is not a C.

2. The isolated pair of polynucleotide primers of claim 1 wherein one of said pair of polynucleotide primers comprises nucleotides 394 and/or 395 of the coding sequence of a human IDH1 protein and the nucleotide 394 of said coding sequence is selected from the group consisting of A and G or nucleotide 395 of said coding sequence is selected from the group consisting of A and T.

3. The isolated pair of polynucleotide primers of claim 1 wherein the coding sequence is of a human IDH2 protein and the nucleotide 515 of said coding sequence is selected from the group consisting of T and A or nucleotide 514 of said coding sequence is a G.

4. The isolated pair of polynucleotide primers of claim 2 wherein nucleotide 394 of said coding sequence is A.

5. The isolated pair of polynucleotide primers of claim 2 wherein nucleotide 394 of said coding sequence is G.

6. The isolated pair of polynucleotide primers of claim 2 wherein nucleotide 395 of said coding sequence is A.

7. The isolated pair of polynucleotide primers of claim 2 wherein nucleotide 395 of said coding sequence is T.

8. The isolated pair of polynucleotide primers of claim 3 wherein nucleotide 515 of said coding sequence is T.

9. The isolated pair of polynucleotide primers of claim 3 wherein nucleotide 515 of said coding sequence is A.

10. The isolated pair of polynucleotide primers of claim 3 wherein nucleotide 514 of said coding sequence is a G.

11. An isolated hybridization probe comprising at least 10 but less than 600 contiguous nucleotide residues of a coding sequence of a human IDH1 or IDH2 protein found in a human tumor or its complement, said at least 10 contiguous nucleic acid residues comprising:
nucleotides 394 and/or 395 of IDH1 coding sequence, wherein said nucleotides are not C or T at nucleotide 394 and/or not G at nucleotide 395;
nucleotide 515 of IDH2 coding sequence, wherein said nucleotide 515 is not a G;
the complement of nucleotides 394 and/or 395 of IDH1 coding sequence, wherein said nucleotides are not C or T at nucleotide 394 and/or not G at nucleotide 395, respectively; or
the complement of nucleotide 515 of IDH2 coding sequence, wherein said nucleotide 515 is not a G, wherein the hybridization probe is labeled with a detectable label.

12. An isolated amplification primer comprising at least 10 but less than 600 contiguous nucleotide residues of a coding sequence of a human IDH1 or IDH2 protein found in a human tumor or its complement, said at least 10 contiguous nucleic acid residues comprising:
nucleotides 394 and/or 395 of IDH1 coding sequence, wherein said nucleotides are not C or T at nucleotide 394 and/or not G at nucleotide 395;
nucleotide 515 of IDH2 coding sequence, wherein said nucleotide 515 is not a G;
the complement of nucleotides 394 and/or 395 of IDH1 coding sequence, wherein said nucleotides are not C or T at nucleotide 394 and/or not G at nucleotide 395, respectively; or
the complement of nucleotide 515 of IDH2 coding sequence, wherein said nucleotide 515 is not a G,

wherein the amplification primer is labeled with a detectable label.

13. The isolated hybridization probe of claim 11 wherein the probe comprises a coding sequence of a human IDH1 protein and nucleotide 394 of said coding sequence is selected from the group consisting of A and G or nucleotide 395 of said coding sequence is selected from the group consisting of A and T.

14. The isolated hybridization probe of claim 13 wherein nucleotide 394 of said coding sequence is A.

15. The isolated hybridization probe of claim 13 wherein nucleotide 394 of said coding sequence is G.

16. The isolated hybridization probe of claim 13 wherein nucleotide 395 of said coding sequence is A.

17. The isolated hybridization probe of claim 13 wherein nucleotide 395 of said coding sequence is T.

18. The isolated hybridization probe of claim 11 wherein the probe comprises the complement of a coding sequence of a human IDH1 protein and nucleotide 394 of said coding sequence is selected from the group consisting of G or A.

19. The isolated polynucleotide primer of claim 12 wherein the primer comprises a coding sequence of a human IDH1 protein and nucleotide 394 of said coding sequence is selected from the group consisting of A and G or nucleotide 395 of said coding sequence is selected from the group consisting of A and T.

20. The isolated polynucleotide primer of claim 19 wherein nucleotide 394 of said coding sequence is A.

21. The isolated polynucleotide primer of claim 19 wherein nucleotide 394 of said coding sequence is G.

22. The isolated polynucleotide primer of claim 19 wherein nucleotide 395 of said coding sequence is A.

23. The isolated polynucleotide primer of claim 19 wherein nucleotide 395 of said coding sequence is T.

24. The isolated polynucleotide primer of claim 12 wherein the probe comprises the complement of a coding sequence of a human IDH1 protein and nucleotide 394 of said coding sequence is selected from the group consisting of G or A.

Assignees

• Univ Johns Hopkins
• Univ Duke

Inventors

• Vogelstein Bert
• Kinzler Kenneth W
• Parsons D Williams
• Zhang Xiaosong
• Lin Jimmy Cheng-Ho
• Leary Rebecca J
• Angenendt Philipp
• Papadopoulos Nickolas
• Velculescu Victor
• Parmigiani Giovanni
• Karchin Rachel
• Jones Sian
• Yan Hai
• Bigner Darell
• Kuan Chien-Tsun
• Riggins Gregory J

Classifications

• A61P35/00

  Antineoplastic agents · CPC title

• A61P37/04

  Immunostimulants · CPC title

• C12Q2600/156

  Polymorphic or mutational markers · CPC title

• C12Q2600/112

  Disease subtyping, staging or classification · CPC title

• C12Q2600/118

  Prognosis of disease development · CPC title